[BioC] expression set object for metaanalysis

[Kasper Daniel Hansen]

Your
  rma_data_selected
is already an ExpressionSet (try class(rma_data_selected)), so you
already have what you want.

Otherwise, your call
  data1<-new("ExpressionSet",exprs=rma_data_selected,phenodata=pData,annotation="hgu133a2")
should be something like
  data1<-new("ExpressionSet",exprs=exprs(rma_data_selected),phenoData=phenoData(rma_data_selected),annotation="hgu133a2")

(I think it is phenoData and not phenodata, but my memory might fail me)

Kasper



On Fri, Jan 14, 2011 at 3:51 PM, Peevi Ijkl <ipeevi at yahoo.com> wrote:
> hello list
> I know i have been asking the same question over and over again but i just want
> to make sure am clear.
> I am loading the CEL files into R using ReadAffy along with the phenodata..then
> I am performing normalization.Now i want to create another expression set object
>
> which I can use for meta-analysis but I am not able to.Any suggestions will be
> helpful.
> thanks
> peevi
>
> pd <- read.AnnotatedDataFrame( "target.txt", header=T, row.names=1, sep=";" )
> pData(pd)
> expression_data <- ReadAffy( filenames = rownames (pData(pd)) )
> expression_data
> rma_expression_data <-rma(expression_data)
> f1 <- function( x ) ( IQR(x) > 0.5 )
> ff <- filterfun(f1)
> rma_filtered <- genefilter( rma_expression_data, ff )
> sum(rma_filtered)
> rma_data_selected <- rma_expression_data [ rma_filtered, ]
> dim(rma_expression_data)
> dim(rma_data_selected)
>
> till here I have no errors at all..after this i try the following..
>
> data1<-new("ExpressionSet",exprs=rma_data_selected,phenodata=pData,annotation="hgu133a2")
>
>
> Error in function (classes, fdef, mtable)  :
>  unable to find an inherited method for function "annotatedDataFrameFrom", for
> signature "ExpressionSet".
>
> please help!
>
>
>
>
>        [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>